Systems and methods to enhance consistency of assay performance

ABSTRACT

Systems and methods are disclosed for enhancing the consistency of performance of assays, such as multiplexed assays, by printing features in a particular pattern, such that the outer edge of the pattern has a shape that is substantially similar to the shape of the test well. For example, the pattern is a ring pattern, such that the outer edge of the ring pattern is circular or oval along the bottom of multiplexed wells. The assay substrates prepared according to the methods described result in more accurate, precise, and sensitive chemical and/or biological analyses.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 13/677,113, filed Nov. 14, 2012, which claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Patent Application No. 61/559,470, filed on Nov. 14, 2011, each of which is incorporated by reference herein in its entirety.

BACKGROUND Field of Invention

The present inventions relate to systems and methods for enhancing the consistency of assay performance, including preparation of assay substrates.

Description of Related Art

An assay substrate is a surface upon which various chemical and/or biological analyses can be performed. Examples of an assay substrate include microarray plates, glass slides, and microtiter plates. A microtiter plate is a flat plate that has multiple “wells” formed in its surface. Each well can be used as a small test tube into which various materials can be placed to perform biochemical analyses. One illustrative use of microtiter plates includes an enzyme-linked immunosorbent assay (ELISA), which is a modem medical diagnostic testing technique.

Generally, in an ELISA, a capture antibody is printed in the bottom of a well in a microtiter plate. The capture antibody has specificity for a particular antigen for which the assay is being performed. A sample to be analyzed is added to the well containing the capture antibody, and the capture antibody “captures” or immobilizes the antigen contained in the sample. A detect antibody is then added to the well, which also binds and/or forms a complex with the antigen. Further materials are then added to the well which cause a detectable signal to be produced by the detect antibody. For example, when light of a specific wavelength is shone upon the well, the antigen/antibody complexes will fluoresce. The amount of antigen in the sample can be inferred based on the magnitude of the fluorescence. In another example, a compound can be added to the well that causes the detect antibody to emit light within a predetermined wavelength (e.g., 400-500 nm). This light can be read by a charged-coupled device (CCD) camera to measure the optical brightness of the emitted light.

During an ELISA, the absorbency, fluorescence, or electrochemical signal of the well can be measured and compared with a standard to more accurately determine the presence and quantity of the sample antigen. For example, a calibration feature with a known concentration of antigen can be placed in wells separate from the wells that receive antigen-containing patient samples. However, signal variability, such as fluorescence variability, and well-to-well variability in the separate wells can decrease the accuracy and reliability of test results. A need exists for methods and systems to provide and improve accuracy, reliability, and sensitivity of medical diagnostic testing techniques and other biochemical analyses.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows an assay well with analysis features arranged in a conventional grid array pattern.

FIGS. 2A-C show a series of cross-sectional side views of a well in a microtiter plate during a known method of conducting an ELISA.

FIG. 3 shows an assay well with analysis features arranged in a ring pattern, such that the outer edge of the ring pattern is circular, in accordance with some embodiments.

FIG. 4 shows a method of preparing assay substrates with analysis features arranged in a pattern in accordance with some embodiments.

DETAILED DESCRIPTION

This disclosure relates to systems and methods to enhance the consistency of performance of assays, such as multiplexed assays, by printing analysis features along the bottom of the well in a pattern, such that the outer edge of the pattern has a shape that is substantially similar to the shape of the test well. In one aspect, the disclosure relates to testing substrates that include a substrate material defining at least one well, the well having a bottom surface and at least one side wall, the at least one side wall having a bottom surface and at least one side wall, the at least one side wall having a cross-sectional shape lying in a plane parallel to the bottom surface; and at least one set of analysis features disposed on the bottom surface in a pattern, the pattern having a shape that is substantially similar to the cross-sectional shape of the at least one side wall. In some embodiments, the pattern of the features is non-rectangular. In some embodiments, the pattern is oval or circular. In some embodiments, the pattern has multiple rings. In other embodiments, the substrate further includes at least one calibration feature printed onto the analysis features, wherein the calibration feature has one or more known concentrations of a compound that binds to the analysis features; and at least one additional analysis feature in the same well of the testing substrate.

The disclosed systems and methods increase the detection capabilities of a biochemical assay. The disclosed systems and methods also increase assay throughput and reduce processing time for running experiments and analyses, as fewer assays must be run because of the increased consistency of performance of the assays. The systems and methods reduce the inaccuracy that can result from signal variability and day-to-day variability. Embodiments of the inventions increase the throughput and efficiency of all biochemical analyses (for example, ELISAs) where the output signal is related to light intensity. Suitable samples for use in assays and other biochemical analyses include, but are not limited to, samples from, for example, cell lysates, cell supernatants, plasma, serum, and other biological fluids.

Conventionally, feature patterns are printed on the bottom of wells in a grid format, such as a rectangular or square pattern. However, one problem with such an approach is that each of the features in the well do not interact in the same manner with the fluid presented in the well due to several circumstances. First, the meniscus effect causes this lack of equivalent interaction. The meniscus is the curve in the upper surface of a liquid close to the surface of a container, such as a test well, and is caused by surface tension. Because of the geometry of the test well, a meniscus forms. Second, when a test plate is static, the volume of fluid remains relatively uniform. However, test plates are often dynamic. Plates are moved when transferred from one place to another during experimentation. Also, plates can be placed on various laboratory equipment, including stir plates. When a plate is shaken or moved, fluid is swirled, which accentuates the meniscus effect. Thus, features in a well are not exposed to the same amount of fluid.

The disclosed systems and methods enhance the consistency of assays by printing features in a pattern that takes into account the factors discussed herein that lead to features not being exposed to the same amount of fluid. In some embodiments, the features are printed in a pattern such that the outer edge of the pattern has a shape that is substantially similar to the shape of the test well. In some embodiments, the pattern of the features is non-rectangular. In some embodiments, the pattern is oval or circular. In other embodiments, the pattern has multiple rings.

The disclosed systems and methods result in assays with increased sensitivity, accuracy, and precision. “Sensitivity” is the ability to detect clinically important but very low levels of, for example, an antibody. The “sensitivity” of an assay can be evaluated by diluting known positive samples sequentially and determining the dilution at which the reaction is lost. Test samples often have low amounts of analyte, and the disclosed systems and methods allow detection of an analyte even with low test samples. The “accuracy” of an assay refers to the ability to measure the quantity of the substance in a test sample to that quantity's actual (true) value. “Precision” refers to the ability of the assay to consistently reproduce a result; it is the degree to which repeated measurements under unchanged conditions show the same results. Intra-assay and inter-assay precision are two distinct measures of this precision.

In a conventional two-dimensional grid pattern, a coefficient of variation (CV) ranges from about 12% to about 15%. The variability of biochemical assays is often summarized by the CV, which is defined as the standard deviation (SD) divided by the mean, with the result often reported as a percentage. One reason to use CV is that the SDs of such assays generally increase or decrease proportionally as the mean increases or decreases, so that division by the mean removes it as a factor in the variability. The CV is a standardization of the SD that allows comparison of variability estimates regardless of the magnitude of analyte concentration, at least throughout most of the working range of the assay. The disclosed methods and systems produce results with CV ranges of about 5% or less, about 4% or less, about 3% or less, about 2% or less, or about 1% or less.

FIG. 1 shows a top view of an assay well with features arranged in a conventional grid array pattern. FIG. 1 is a top view of one well 100 in, for example, a microtiter-based platform. In one illustrative implementation, the well substrate is formed of a polystyrene base. Other potential substrate materials include, but are not limited to, nitrocellulose, glass, and other plastic materials. During the preparation of a microtiter plate for use in biochemical analysis, many different analysis “features” 110, including capture antibody features or analyte features, are printed in the well and adhere to the polystyrene base of the well. As used herein, “features” can have different shapes, such as, for example, a rounded shape. The assay substrate can be, for example, a 96-well or 384-well microtiter plate. The diameter of each of the features can be, for example, about 250 μm to about 800 μm in diameter, from about 350 μm to about 700 μm, to about 600 μm. In one example, the CV for a 3×3 9 Plex IL-6 array with a conventional grid pattern is 14.0%. The distance 120 from a center of one analysis feature to a center of an adjacent analysis feature ranges from about 909 μm to about 1100 μm, to about 1050 μm. The diameter of well 100 ranges from about 5000 μm to about 7000 μm, to about 6580 μm.

The disclosed methods and systems produce results with CV ranges of about 5% or less. FIG. 3 shows a top view of an assay well 300 with features 310 arranged in ring pattern 340, wherein an outer edge of the ring pattern is circular, in accordance with some embodiments. The well 300 has a bottom surface 350 and a side wall 360. In some embodiments, one assay well has a range of 8 to 16 analysis features, 10 to 14 features, to 12 features. In FIG. 3, there are 12 analysis features 310 in a ring pattern 340, wherein an outer edge of the ring pattern is circular. Using a 8-plex IL-6 array with a ring pattern as shown in FIG. 3, the CV was tested to be only 2.4%, a more than 5-fold improvement over conventional grid patterns. In one embodiment, the features are printed in a circular pattern, such that the radial distance from the center of the feature to the center of the well is substantially the same for each feature. In some embodiments, the diameter of the well 300 ranges from about 1.5 mm to about 6.86 mm, from about 2.4 mm to about 6.4 mm, and is about 6.58 mm. In some embodiments, the angle 330 formed by, for example, lines 320, is about 30.° In some embodiments, the diameter of each of the features can be, for example, about 250 μm to about 800 μm in diameter, about 350 μm to about 700 μm, to about 600 μm. In some embodiments, the radius of the circle 340 is about 1 to about 3 mm, about 1.5 to about 2.5 mm, is about 1.93 mm.

During the preparation of a microtiter plate for use in biochemical analysis, many different analysis “features” 110, including capture antibody features or analyte features, are printed in the well and adhere to the polystyrene base of the well. As used herein, “features” can have different shapes, such as, for example, a rounded shape. The assay substrate can be, for example, a 96-well or 384-well microtiter plate. The diameter of each of the features can be, for example, about 250 μm to about 800 μm in diameter, from about 350 μm to about 700 μm, to about 600 μm. In one example, the CV for a 3×3 9 Plex IL-6 array with a conventional grid pattern is 14.0%. The distance 120 from a center of one analysis feature to a center of an adjacent analysis feature ranges from about 909 μm to about 1100 μm, to about 1050 μm. The diameter of well 100 ranges from about 5000 μm to about 7000 μm, to about 6580 μm.

In some embodiments, the features are far enough from the outer edge of the well so that the features are exposed to approximately the same amount of fluid, taking into account the meniscus effect and the effects of moving the well. In some embodiments, the distance from the edge of the well to the center of the feature is about 10% to about 90% of the radius of the well. In other embodiments, the distance from the edge of the well to the center of the feature is about 20% to about 80%, about 30% to about 70%, about 40% to about 60%, and about 50% of the radius of the well. In some embodiments, an angle, shown as 310, is formed by a first line that extends from the center of one feature to the center of the well and a second line that extends from the center of an adjacent feature to the center of the well, and the angle is substantially the same for each adjacent feature.

FIG. 2 show a series of cross-sectional side views 200 of a well 205 during a known method of conducting an ELISA. The description of methods of conducting biochemical analyses such as an ELISA using in-well calibration features is described in International Application No. PCT/US2011/061184, entitled Method of and System for Printing In-Well Calibration Features, filed on Nov. 17, 2011, and is incorporated by reference herein. Only one feature is shown in FIG. 2A for clarity, but it is understood that embodiments of the inventions include features printed around the bottom of the well, such as in a circular or oval pattern. In some embodiments, after the capture antibody feature 210 has been printed onto the bottom of the well 205, a blocking material is added to the well to block plate binding sites 215 that remain on the plate 200. This prevents non-selective binding of sample antigens to the base of the well during the ELISA, which would give false readings. Second, an antigen-containing sample is added to the well. FIG. 2B shows the antigen 220 binding to the capture antibody feature 210. Third, the well is washed so that unbound antigen is removed. Fourth, enzyme linked detect antibodies are added. FIG. 2C shows the enzyme-linked detect antibody 230 binding to the antigen 220. The well is then washed so that unbound antibody-enzyme conjugates are removed. Next, a substance is applied which converts the enzyme into a detectable signal, such as a color, fluorescent, or electrochemical signal. Finally, the absorbency, fluorescence, or electrochemical signal of the well is measured and compared with a standard to determine the presence and quantity of the sample antigen. A standard can be generated by printing calibration features with a known concentration of antigen in wells that are separate from or the same as the wells that receive patient samples.

Multiplexed immunoassays include forward-phase techniques, where the target protein is detected by using direct labeling, or sandwich assay techniques, as described above with the ELISA technique, where the target protein is detected using a secondary-labeled antibody. However, the disclosure herein is not limited to forward-phase or sandwich techniques and includes the application of reverse-phase techniques. In reverse-phase arrays, an antigen containing sample (including but not limited to from cell lines, tissue samples, blood samples, or any other source of proteomic material) is first added to the well, followed by wash steps and the addition of antibodies that are detected.

FIG. 4 shows a method 400 of preparing assay substrates in accordance with some embodiments. As discussed herein, although FIG. 4 describes a sandwich assay techniques, the instant disclosure encompasses other assay techniques known in the art, including forward phase and reverse-phase techniques. In the instant disclosure, by printing features with specific patterns, such as circular or oval patterns, method 400 reduces or eliminates the inaccuracy and imprecision that can result from signal variability and well-to-well variability. Not only does method 400 reduce the variance of assay results, it also increases throughput, as consistency of the assay results reduces the number of times that analyses must be run to obtain accurate and precise results.

As used herein, a “target plate” is a plate that is to be prepared (for example, printed, blocked, and processed for later usage) for a particular set of analyses. A “source plate” is a plate that has a supply of the material to be printed onto a target plate. For example, the wells of a source plate can be filled with various types of antibodies that are to be printed onto target plates. In accordance with method 400, the source plate is prepared for the printing process (step 410). This can include filling the wells of the source plate with the desired material to be printed onto the target plate. Next, the target plate is prepared for printing (step 420). This can include washing and/or performing other surface treatments to enable the material to be printed to properly adhere to the bottom surface of the plate well.

The source and target plates are then fit into a printing apparatus (for example, a 2470 Arrayer available from Aushon Biosystems, Inc. of Billerica, Mass.) (step 430). In some embodiments, capture antibody features are printed in the wells of the target plate according to any of the patterns disclosed herein (step 440). In some embodiments, the outer edge of the pattern has a shape that is substantially similar to the shape of the test well. In some embodiments, the pattern of the features is non-rectangular. In some embodiments, the pattern is oval or circular. In other embodiments, the pattern has multiple rings.

In some embodiments, the features are printed in a circular pattern, such that the radial distance of the center of the feature to the center of the well is substantially the same for each of the features. The features are printed far enough from the edge of the well so that the features are exposed to approximately the same amount of fluid. Although not bound by any theory, the features are spaced from the edge of the well to avoid signal cross talk with nonspecific binding occurring at the junction of the well wall and well bottom. The accuracy of automated feature identification and data extraction algorithms is decreased when the features are too close to the well wall—the non-specific binding at the well wall/bottom junction confuses the algorithms, causing the non-specific binding to be identified as the “feature” instead of the actual feature. In some embodiments, the distance from the outer edge of the well to the center of the feature is about 10% to about 90% of the radius of the well. In other embodiments, the distance from the outer edge of the well to the center of the feature is about 20% to about 80%, about 30% to about 70%, about 40% to about 60%, and about 50% of the radius of the well.

Optionally, calibration features with a known concentration of an antigen are precisely printed onto the capture antibody features (step 450). The known concentration of an antigen ranges from the order of femtogram (10⁻¹⁵ g) per milliliter to milligram (10⁻³ g) per milliliter. This print step using the load printing apparatus (e.g., the 2470 Arrayer), independent of the pins size of the apparatus, can print the calibration features precisely onto the capture antibody features in the disclosed patterns. In some cases, the positional misalignment between the calibration features and the capture antibody features is about 4 μm or less. Positional misalignments between the calibration features and the capture antibody features of greater than about 4 μm, depending on the size of the features, can also be tolerated. For example, when printing features are in the range of about 120 μm to about 240 μm in diameter, positional misalignment between the calibration features and the capture antibody features of about 10 μm can be tolerated.

In some embodiments, the printed target plate is incubated for a period of time (step 460), and a blocking material, which does not react to the capture antibody, is applied to the target plate using known methods (step 470). The blocking material adsorbs to the remaining binding surfaces of the plate and binds to antigens of non-specific interaction, thus reducing background signal. The printed target plate is then dried (step 480). In one illustrative implementation, a blocking material solution is applied to the surfaces of the bottoms of a plurality of wells in a microtiter plate via a spraying process, as described in U.S. patent application Ser. No. 13,206,775, entitled Method of and System for Applying Blocking Material to Assay Substrates, filed on Aug. 10, 2011, the contents of which are incorporated by reference in its entirety.

In some embodiments, the target plate is then processed for usage or storage using known methods (step 490). For example, the target plate can be incubated at about 4° C. overnight. Alternatively, excess blocking material (e.g., the blocking material that has not bound to the bottom of the well) can be removed from the target plate, the plate can then be dried, and then the plate can be placed into a moisture-resistant package for storage. The plates can then be used to conduct chemical and/or biological analyses, such as with an ELISA.

The specific operational parameters provided above are merely illustrative, and other values are within the scope of the inventions.

Kits can be made that incorporate the systems described herein along with any combination of related equipment or reagents, such as reporter reagents or software for reading results of the assay.

The embodiments described above can be used to detect the presence of antigens and proteins in a patient, such as a patient having an autoimmune disease, antibodies to viral diseases, antibodies to bacterial diseases, antibodies to allergic reactions, or antibodies to cancers.

The terms and expressions that are employed herein are terms of description and not of limitation. There is no intention in the use of such terms and expressions of excluding the equivalents of the feature shown or described, or portions thereof, it being recognized that various modifications are possible within the scope of the inventions as claimed. 

1.-25. (canceled)
 26. A testing substrate comprising: a substrate material defining at least one well, the at least one well having a bottom surface, a center, and at least one side wall, the at least one side wall having a cross-sectional shape when lying in a plane parallel to the bottom surface; and a set of analysis features on the bottom surface in a pattern, characterized in that the pattern has multiple circular rings of analysis features, wherein each ring of the multiple rings of analysis features has a shape similar to the cross-sectional shape of the side wall, wherein for each ring of the multiple rings of analysis features, a distance from the outer edge of the at least one well to the center of each of the analysis features is about 20% to about 80% of a radius of the at least one well.
 27. The substrate of claim 26, wherein for each ring of the multiple rings of analysis features, all of the analysis features of the ring are arranged such that a distance from a center of each of the features to the center of the well is the same for each of the features.
 28. The substrate of claim 26, wherein for each ring of the multiple rings of analysis features, the analysis features of the ring are arranged such that an angle is formed by a first line that extends from the center of one feature to the center of the at least one well and a second line that extends from the center of an adjacent feature to the center of the at least one well, wherein the angle is the same for each adjacent line.
 29. The substrate of claim 26, wherein for each ring of the multiple rings of analysis features, a distance from the outer edge of the at least one well to the center of each of the analysis features is about 30% to about 70% of the radius of the at least one well.
 30. The substrate of claim 26, wherein an entirety of the bottom surface is substantially flat.
 31. The substrate of claim 26, wherein the analysis features of the set of analysis features are printed on the bottom surface.
 32. The substrate of claim 26, wherein at least one ring of the multiple rings of analysis features has 8 to 16 analysis features.
 33. The substrate of claim 26, wherein each of the analysis features of the set of analysis features has a diameter of about 250 micrometers to about 800 micrometers.
 34. The substrate of claim 26, wherein at least some of the analysis features comprise an antibody.
 35. A method for forming a testing substrate, comprising: forming a set of analysis features on the bottom surface of a well of the testing substrate, the well having a bottom surface, a center, and at least one side wall, the at least one side wall having a cross-sectional shape when lying in a plane parallel to the bottom surface, and wherein the analysis features are arranged in a pattern, characterized by multiple circular rings of analysis features, wherein each ring of the multiple rings of analysis features has a shape similar to the cross-sectional shape of the side wall, wherein for each ring of the multiple rings of analysis features, a distance from the outer edge of the at least one well to the center of each of the analysis features is 10% to 90% of a radius of the at least one well.
 36. The method of claim 35, wherein for each ring of the multiple rings of analysis features, all of the analysis features of the ring are arranged such that a distance from a center of each of the features to the center of the well is the same for each of the features.
 37. The method of claim 35, wherein for each ring of the multiple rings of analysis features, the analysis features of the ring are arranged such that an angle is formed by a first line that extends from the center of one feature to the center of the at least one well and a second line that extends from the center of an adjacent feature to the center of the at least one well, wherein the angle is the same for each adjacent line.
 38. The method claim 35, wherein for each ring of the multiple rings of analysis features, a distance from the outer edge of the at least one well to the center of each of the analysis features is about 30% to about 70% of the radius of the at least one well.
 39. The method of claim 35, wherein an entirety of the bottom surface is substantially flat.
 40. The method of claim 35, wherein the step of forming the set of analysis features comprises printing the set of analysis features on the bottom surface.
 41. The method of claim 35, wherein at least one ring of the multiple rings of analysis features has 8 to 16 analysis features.
 42. The method of claim 35, wherein each of the analysis features of the set of analysis features has a diameter of about 250 micrometers to about 800 micrometers.
 43. The method of claim 35, wherein at least some of the analysis features comprise an antibody.
 44. The method of claim 29, further comprising: incubating the testing substrate; applying blocking material to the testing substrate on which the set of analysis features is provided; drying the testing substrate; and processing the testing substrate for usage or storage. 